Merge pull request #450 from LIHPC-Computational-Geometry/449-repositories-restructuration

Code restructuration

Author: nicolaslg

.circleci/config.yml

@@ -57,7 +57,7 @@ jobs:
         cmake /__w/gmds/gmds -DCMAKE_BUILD_TYPE=${{ matrix.config }} 
         -DWITH_CODE_COVERAGE:BOOL=ON
         -DWITH_CGNS:BOOL=OFF
-        -DWITH_PYTHON_API:BOOL=ON
+        -DWITH_PYTHON_API:BOOL=OFF
         -DWITH_TEST:BOOL=ON
         -DENABLE_BLOCK_MESHER:BOOL=ON
         -DENABLE_BLOCKING:BOOL=ON

.github/workflows/continuous-ubuntu.yml

@@ -22,9 +22,6 @@ build*/
 # other modifications should be carefully considered.
 # comment when necessary
 external/
-#!external/glpk/src/glpk/w64/glpk_4_65.dll
-#!external/glpk/src/glpk/w64/glpk_4_65.lib
-
 
 # spack files when dev-build
 spack-build*

.gitignore

@@ -142,7 +142,7 @@ add_subdirectory(external/HLBFGS)
 
 GMDS_ADD_COMPONENT(
         BLOCK_MESHER                       # cmake variable
-        blockMesher                        # src subdirectory name
+        sandbox/blockMesher                        # src subdirectory name
         GMDSBlockMesher                    # name of the generated library
         "Provide the mesh of a block structure classified on a CAD geometry"  # description
         OFF                                # is activated
@@ -151,35 +151,26 @@ GMDS_ADD_COMPONENT(
 
 GMDS_ADD_COMPONENT(
         MCTSBLOCK                       # cmake variable
-        mctsblock                        # src subdirectory name
+        sandbox/mctsblock                        # src subdirectory name
         GMDSMctsBlock                    # name of the generated library
         "Blocking generation using MCTS"  # description
         OFF                                # is activated
         OFF                                 # must be covered
 )
 
 
-GMDS_ADD_COMPONENT(
-        BLOCKING                       # cmake variable
-        blocking                        # src subdirectory name
-        GMDSBlocking                    # name of the generated library
-        "This module provides a data structure for a blocking representation"  # description
-        ON                                 # is activated
-        ON                                 # must be covered
-)
-
 GMDS_ADD_COMPONENT(
         AERO                       # cmake variable
-        aero                        # src subdirectory name
+        modules/aero                        # src subdirectory name
         GMDSAero                    # name of the generated library
-        " "  # description
+        "Advancing front algorithm (2D/3D) dedicated to atmosphere re-entry "  # description
         ON                                # is activated
         ON                                 # must be covered
 )
 
 GMDS_ADD_COMPONENT(
         DUAL_BLOCKING
-        dualBlocking
+        sandbox/dualBlocking
         GMDSDualBlocking
         "Dual blocking component"
         OFF
@@ -188,16 +179,16 @@ GMDS_ADD_COMPONENT(
 
 GMDS_ADD_COMPONENT(
         ELG3D
-        Elg3D
+        modules/Elg3D
         GMDSelg3d
         "overlay-grid algorithm"
         OFF
         OFF                                 # must be covered
 )
 
 GMDS_ADD_COMPONENT(
-        ELGMORPHING
-        elgmorphing
+        ELG_MORPHING
+        modules/elgmorphing
         GMDSelgmorphing
         "morphing the mesh"
         OFF
@@ -206,7 +197,7 @@ GMDS_ADD_COMPONENT(
 
 GMDS_ADD_COMPONENT(
         FRAME                               # cmake variable
-        frame                               # src subdirectory name
+        modules/frame                               # src subdirectory name
         GMDSFrame                           # name of the generated library
         "Frame field generation component"  # description
         ON                                 # is activated
@@ -215,7 +206,7 @@ GMDS_ADD_COMPONENT(
 
 GMDS_ADD_COMPONENT(
         FRAME_3D
-        frame3d
+        modules/frame3d
         GMDSFrame3d
         "3D Frame field generation component"
         ON
@@ -224,16 +215,16 @@ GMDS_ADD_COMPONENT(
 
 GMDS_ADD_COMPONENT(
         GEOD_HONEY_COMB
-        geodHoneyComb
+        modules/geodHoneyComb
         GMDSGeodHoneyComb
         "Algorithms to create honeycomb like meshes for spherical geometries"
         ON
         ON                                # must be covered
 )
 
 GMDS_ADD_COMPONENT(
-        HYBRIDMESHADAPT
-        hybridMeshAdapt
+        HYBRID_MESH_ADAPT
+        sandbox/hybridMeshAdapt
         GMDSHybridMeshAdapt
         "Hybrid remeshing component"
         OFF
@@ -242,16 +233,17 @@ GMDS_ADD_COMPONENT(
 
 GMDS_ADD_COMPONENT(
         KMDS
-        kmds
+        modules/kmds
         GMDSkmds
         "kokkos-based mesh structure"
         OFF
         OFF                                 # must be covered
 )
 
+
 GMDS_ADD_COMPONENT(
-        MEDIALAXIS
-        medialaxis
+        MEDIAL_AXIS
+        modules/medialaxis
         GMDSMedialaxis
         "Medial-axis component"
         OFF
@@ -260,16 +252,24 @@ GMDS_ADD_COMPONENT(
 
 GMDS_ADD_COMPONENT(
         MEDUSA
-        medusa
+        sandbox/medusa
         GMDSMedusa
         "Visualization component"
         OFF
         OFF                                 # must be covered
 )
+GMDS_ADD_COMPONENT(
+        SHEET
+        sandbox/sheet
+        GMDSSheet
+        "Sheet operation for quad/hex meshes"
+        OFF
+        OFF                                 # must be covered
+)
 
 GMDS_ADD_COMPONENT(
         MILP
-        milp
+        sandbox/milp
         GMDSmilp
         "Mixed-Integer Linear Programming component"
         OFF
@@ -278,7 +278,7 @@ GMDS_ADD_COMPONENT(
 
 GMDS_ADD_COMPONENT(
         MORPHMESH
-        morphMesh
+        modules/morphMesh
         GMDSmorphMesh
         "morphing the mesh"
         ON
@@ -287,43 +287,43 @@ GMDS_ADD_COMPONENT(
 
 GMDS_ADD_COMPONENT(
         PADDING
-        padding
+        sandbox/padding
         GMDSPadding
         "Smart Padding/Pillowing algorithm"
         OFF
-        ON                                # must be covered
+        OFF                                # must be covered
 )
 
 GMDS_ADD_COMPONENT(
         POLYBLOCK
-        polyblock
+        sandbox/polyblock
         GMDSPolyblock
         "Polycube_like algorithms for hexahedral blocking"
         OFF
-        ON                                # must be covered
+        OFF                                # must be covered
 )
 
 GMDS_ADD_COMPONENT(
         QUADFRONT                               # cmake variable
-        quadfront                               # src subdirectory name
+        sandbox/quadfront                               # src subdirectory name
         GMDSquadfront                           # name of the generated library
         "advancing-front quad mesher"  # description
         OFF                                 # is activated
-        ON                                 # must be covered
+        OFF                                 # must be covered
 )
 
 GMDS_ADD_COMPONENT(
         RLBLOCKING                       # cmake variable
-        rlBlocking                       # src subdirectory name
+        sandbox/rlBlocking                       # src subdirectory name
         GMDSRlBlocking                    # name of the generated library
         "MCTS-guided blocking modifications"  # description
         OFF                                 # is activated
         OFF                                 # must be covered
 )
 
 GMDS_ADD_COMPONENT(
-        SINGGRAPHBUILD
-        singGraphBuild
+        SING_GRAPH_BUILD
+        modules/singGraphBuild
         GMDSSingGraphBuild
         "Singularity graph building component"
         ON
@@ -406,25 +406,25 @@ endif(WITH_CODE_COVERAGE)
 #==============================================================================
 #for each component, we define a library name to use and a directory
 set(LIB_GMDS_UTILS GMDSUtils)
-add_subdirectory(utils)
+add_subdirectory(core/utils)
 set(LIB_GMDS_MATH GMDSMath)
-add_subdirectory(math)
+add_subdirectory(core/math)
 set(LIB_GMDS_IG GMDSIg)
-add_subdirectory(ig)
+add_subdirectory(core/ig)
 set(LIB_GMDS_IO GMDSIo)
-add_subdirectory(io)
+add_subdirectory(core/io)
 set(LIB_GMDS_IG_ALGO GMDSIgAlgo)
-add_subdirectory(igalgo)
+add_subdirectory(core/igalgo)
 set(LIB_GMDS_QUALITY GMDSQuality)
-add_subdirectory(quality)
+add_subdirectory(core/quality)
 set(LIB_GMDS_CAD GMDSCad)
-add_subdirectory(cad)
+add_subdirectory(core/cad)
 set(LIB_GMDS_CADFAC GMDSCadFac)
-add_subdirectory(cadfac)
+add_subdirectory(core/cadfac)
+set(LIB_GMDS_BLOCKING GMDSBlocking)
+add_subdirectory(core/blocking)
 set(LIB_GMDS_SMOOTHY GMDSSmoothy)
-add_subdirectory(smoothy)
-set(LIB_GMDS_IG_SHEET GMDSSheet)
-add_subdirectory(sheet)
+add_subdirectory(core/smoothy)
 
 if(WITH_PYTHON_API)
     add_subdirectory(pygmds)

CMakeLists.txt

@@ -19,7 +19,7 @@ This project is part of the [magix3d](https://github.com/LIHPC-Computational-Geo
 ## Last changes
 - We changed our installation procedure. In particular, we externalized some of gmds depencies. See the [developer documentation](docs/mkdocs/dev-guide/developers_doc.md) for more details.
 - Important work is done on the Python API, see the [pygmds](pygmds/README.md) module.
-- Our blocking structure is evolving to be more robust and efficient for the blocking procedure. See the [blocking](blocking/README.md) module.
+- Our blocking structure is evolving to be more robust and efficient for the blocking procedure. See the [blocking](core/blocking/README.md) module.
 
 ## GMDS in a nuthsell
 **GMDS**, for **G**eneric **M**esh **D**ata & **S**ervices,  is a C++ library written to provide mesh data structures and algorithms to developers that intend to design meshing algorithms and build pipelines of those algorithms.
@@ -48,24 +48,12 @@ for(auto node_id: m->nodes()){
 ```
 *gmds* provides a framework for developing new algorithms and our current interest is about structured quadrilateral and hexahedral meshing. To generate such meshes, we focus on the following *technologies*:
 - **Frame Fields**. 3 modules are currenly dedicated to the usage of frame fields fo meshing
-    - the [frame](docs/mkdocs/user-guide/frame.md) module provides algorithms for 2D meshing. It relies on the notion of cross fields (see the [math](math/README.md) component for cross definitions). Output of this module are 2D cross fields defined on an input simplex mesh.
+    - the [frame](docs/mkdocs/user-guide/frame.md) module provides algorithms for 2D meshing. It relies on the notion of cross fields (see the [math](core/math/README.md) component for cross definitions). Output of this module are 2D cross fields defined on an input simplex mesh.
     - the [singGraphBuild](docs/mkdocs/user-guide/singgraphbuild.md) module provides algorithm to extract the **base complex** structure of a 2D frame field
     - the [frame3d](docs/mkdocs/user-guide/frame3d.md) module provides algorithms for 3D frame field generation. Unlike the 2D case, we are not able to generate a full block structure but such fields are used to drive hybrid mesh generation and point generation algorithms. 
 - [Overlay grids algorithms](docs/mkdocs/user-guide/elg3d.md).
 - [Sheet operations](docs/mkdocs/user-guide/sheet.md). This module provides sheet operations for quad and hex meshes.
-### A service-based approach
-In order to build and prototype secure pipeline algorithms, we propose a **service** module to assemble our algorithms into a verified and dynamically-secured pipeline. We strongly believe that a main drawback of research but also production codes is that they're are written by researchers in mathematics, physics or computer science who focuses on the application "business" without taking care of "software engineering". This is quite usual and understandable but such a behaviour has 2 main consequences:
-1. Codes are not
-### Algorithms for quad and hex meshing
-GMDS is our ma robust enough because the specification of their input and output are often fuzzy, only known by the main developer;
-2. It is difficult to reuse an algorithm written by someone else.
-
-The **service** module is an answer to this issue. Input and output of each service must be totally specified using a constraint system that is dynamically checked at execution time.
 
 ## Users and developers documentation
 
-Documentation is under construction. we just start to write it. It is split between:
-- [Users documentation](docs/mkd/users_doc.md), which is dedicated to people who want to use **gmds** as a set of libraries but do not expect to contribute to it.
-- [Developers documentation](docs/mkd/developers_doc.md), which is dedicated to developers who would like to create a new *gmds* module for instance. In particular, we explain the [git workflow](docs/mkd/git_workflow.md) that we adopted.
-- Gitub pages are under construction and available [here](https://lihpc-computational-geometry.github.io/gmds).
-- The associated doygen documenation is [here](https://lihpc-computational-geometry.github.io/gmds/doxygen/index.html).
+Documentation is under construction, you can see it [here](https://lihpc-computational-geometry.github.io/gmds). The associated doygen documenation is [here](https://lihpc-computational-geometry.github.io/gmds/doxygen/index.html).